Extending the models for XX and XO data, so as to keep a consensus network as far as possible.

Steps to find the common link to be added :
1.) Read in the extension.csv for both cell lines
2.) Remove links from TFs and Ligands
3.) Retain only links that have adjusted p-value < 0.05 and value !=0
4.) Calculate %improvement in residual for each cell line
5.) Find the intersection list,(Links that appear in both lists)
6.) Calculate the sum of %improvement in residual
7.) Order the intersection list by descending order of sum of %improvement in residual.
8.) Add the link with Max sum of %improvement to both models.

XX

Initial-Fit

Model residual = 2056

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 178 Gsk3 Igfr 1.41636977318046 1278.0453997103 18 778.256069472481 2 0 0
2 171 Gsk3 Akt 2.00694646493033 1288.71986330493 18 767.581605877854 2 0 0
3 183 Gsk3 Pi3k 12.4847203077964 1289.13266471349 18 767.16880446929 2 0 0
4 176 Gsk3 Fgfr 0.191504350700091 1372.05906770831 18 684.242401474471 2 0 0
5 409 Stat3 Igfr 0.996753616400567 1503.11324611178 17 553.188223070994 1 0 0
6 220 Jak Igfr 0.0423204835133162 1503.11324646819 17 553.188222714585 1 0 0
7 407 Stat3 Fgfr 0.300442595039564 1515.31854378356 17 540.982925399222 1 0 0
8 218 Jak Fgfr 0.0127734424506346 1515.31854382344 17 540.982925359343 1 0 0
9 225 Jak Pi3k 0.296100687336135 1519.0225778574 17 537.278891325377 1 0 0
10 414 Stat3 Pi3k 7.25375600064241 1519.02257842854 17 537.278890754242 1 0 0
11 402 Stat3 Akt 0.536041524320762 1523.34265156171 17 532.958817621071 1 0 0
12 213 Jak Akt 0.0227562692432519 1523.34265163465 17 532.958817548128 1 0 0
13 92 Bmp4r Fgfr 100.000006433552 1854.77449407012 18 201.52697511266 2 0 0
14 29 Actr Fgfr -0.792431254842106 1894.64741079159 17 161.65405839119 1 0 0
15 8 Activin Fgfr -0.792421730303328 1894.64741079639 17 161.65405838639 1 0 0
16 386 Smad2 Fgfr -2.41661304775863 1894.64741080543 17 161.654058377349 1 0 0
17 27 Actr Erk -0.753278152279655 1908.45360143645 17 147.84786774633 1 0 0
18 384 Smad2 Erk -2.29713647308538 1908.4536014576 17 147.847867725176 1 0 0
19 6 Activin Erk -0.753278263852543 1908.4536014872 17 147.84786769558 1 0 0
20 34 Actr Mek -0.179931242665053 1930.52896307734 17 125.772506105435 1 0 0

LA1:Jak -> Fgfr

Model residual = 1515

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 178 Gsk3 Igfr 1.13373223613369 971.916732794124 19 543.085239462453 2 0 0
2 171 Gsk3 Akt 1.68288981131664 980.754739533484 19 534.247232723093 2 0 0
3 183 Gsk3 Pi3k 0.947924393614379 981.104897604199 19 533.897074652378 2 0 0
4 176 Gsk3 Fgfr 0.0366389137635851 1042.99093603982 19 472.011036216759 2 0 0
5 179 Gsk3 Jak 4.82607049417883 1186.00515980427 19 328.996812452307 2 0 0
6 180 Gsk3 Lifr 4.82606435685739 1186.00515982395 19 328.996812432625 2 0 0
7 92 Bmp4r Fgfr 10.000011664356 1379.2932140092 19 135.708758247377 2 0 0
8 95 Bmp4r Jak 0.112685439947665 1405.40002964801 19 109.601942608565 2 0 0
9 96 Bmp4r Lifr 18.7278342430109 1405.40002973672 19 109.60194251986 2 0 0
10 90 Bmp4r Erk 1.00371147137984 1409.88137312401 19 105.12059913257 2 0 0
11 6 Activin Erk -0.615067013395841 1431.05413342927 18 83.9478388273039 1 0 0
12 384 Smad2 Erk -1.87566874303168 1431.05413364244 18 83.947838614137 1 0 0
13 27 Actr Erk -0.615067848926145 1431.0541336497 18 83.9478386068793 1 0 0
14 97 Bmp4r Mek 9.99999873272895 1432.52845598323 19 82.4735162733441 2 0 0
15 100 Bmp4r Raf 9.99999873272895 1432.52845598323 19 82.4735162733441 2 0 0
16 101 Bmp4r Ras 9.99999873272895 1432.52845598323 19 82.4735162733441 2 0 0
17 409 Stat3 Igfr 7.56002309560712 1435.74300310753 18 79.2589691490498 1 0 0
18 220 Jak Igfr 0.277563025962606 1435.74303253277 18 79.2589397238112 1 0 0
19 29 Actr Fgfr -0.183059033411394 1436.60116938852 18 78.4008028680528 1 0 0
20 386 Smad2 Fgfr -0.558228312056101 1436.60116941083 18 78.4008028457499 1 0 0

LA2:Gsk3->Igfr

Model residual = 971

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 92 Bmp4r Fgfr 10.000000002636 840.90656890077 21 130.152766430204 2 0 0
2 90 Bmp4r Erk 100 867.875548005494 21 103.183787325481 2 0 0
3 95 Bmp4r Jak 10.0000199775758 878.991505948386 21 92.0678293825883 2 0 0
4 96 Bmp4r Lifr 20.6762188251558 884.153016222639 21 86.9063191083358 2 0 0
5 6 Activin Erk -0.607284252384005 886.422013469847 20 84.6373218611279 1 0 0
6 97 Bmp4r Mek 1.00516042169855 889.305025208258 21 81.754310122717 2 0 0
7 100 Bmp4r Raf 1.00516042169855 889.305025208258 21 81.754310122717 2 0 0
8 101 Bmp4r Ras 1.00516042169855 889.305025208258 21 81.754310122717 2 0 0
9 27 Actr Erk -0.327920236864419 900.199275951258 20 70.8600593797163 1 0 0
10 384 Smad2 Erk -1 900.199275951258 20 70.8600593797163 1 0 0
11 219 Jak Gsk3 0.000109183974943886 902.009674131321 20 69.0496611996534 1 1.11022302462516e-16 3.7858605139718e-14
12 402 Stat3 Akt 0.000183976136582064 902.294992099857 20 68.7643432311172 1 1.11022302462516e-16 3.7858605139718e-14
13 414 Stat3 Pi3k 2.27365794505561e-05 902.378786528824 20 68.6805488021503 1 1.11022302462516e-16 3.7858605139718e-14
14 409 Stat3 Igfr 4.7664504709844e-05 902.459020772464 20 68.6003145585105 1 1.11022302462516e-16 3.7858605139718e-14
15 225 Jak Pi3k 3.88421914391621e-06 902.563706988332 20 68.4956283426425 1 1.11022302462516e-16 3.7858605139718e-14
16 213 Jak Akt 2.65120247787806e-05 902.706281123591 20 68.3530542073835 1 1.11022302462516e-16 3.7858605139718e-14
17 408 Stat3 Gsk3 3.38167487121728e-05 902.715804096824 20 68.3435312341508 1 1.11022302462516e-16 3.7858605139718e-14
18 220 Jak Igfr 2.51416619947405e-05 902.74641391574 20 68.3129214152348 1 1.11022302462516e-16 3.7858605139718e-14
19 13 Activin Mek -0.143412115159229 903.755935338498 20 67.3033999924768 1 2.22044604925031e-16 7.57172102794356e-14
20 16 Activin Raf -0.143412115159229 903.755935338498 20 67.3033999924768 1 2.22044604925031e-16 7.57172102794356e-14

LA3:Actr->Erk

Model residual = 886

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 92 Bmp4r Fgfr 99.9999999999588 796.313518637685 22 89.8968432532421 2 0 0
2 402 Stat3 Akt 0.00119297417254529 798.589911953017 21 87.6204499379104 1 0 0
3 408 Stat3 Gsk3 0.000184583924855102 800.080207927309 21 86.1301539636179 1 0 0
4 213 Jak Akt 0.000128881753807159 800.195130937343 21 86.0152309535839 1 0 0
5 414 Stat3 Pi3k 9.86151801328131e-05 800.214996955867 21 85.9953649350604 1 0 0
6 225 Jak Pi3k 3.66603038374059e-05 800.238242682991 21 85.972119207936 1 0 0
7 219 Jak Gsk3 0.000100636888049157 800.260126458861 21 85.9502354320664 1 0 0
8 220 Jak Igfr 3.39105818481974e-05 800.268301976362 21 85.9420599145651 1 0 0
9 409 Stat3 Igfr 0.000101297690360918 800.444107895457 21 85.76625399547 1 0 0
10 415 Stat3 Raf -0.32150927316615 809.319501337656 21 76.890860553271 1 0 0
11 412 Stat3 Mek -0.321509250512534 809.319504855529 21 76.8908570353983 1 0 0
12 416 Stat3 Ras -0.321509249733861 809.319504957465 21 76.8908569334618 1 0 0
13 227 Jak Ras -0.22623721094403 809.940411606709 21 76.2699502842181 1 0 0
14 226 Jak Raf -0.226237244636066 809.94042527694 21 76.2699366139867 1 0 0
15 223 Jak Mek -0.226237515601056 809.940519470594 21 76.2698424203328 1 0 0
16 90 Bmp4r Erk 10.0000000042663 823.436150807311 22 62.7742110836156 2 2.34257058195908e-14 7.96473997866087e-12
17 95 Bmp4r Jak 10.0000009200621 826.692896942169 22 59.5174649487577 2 1.19126930542279e-13 4.05031563843749e-11
18 96 Bmp4r Lifr 141.348000474156 829.147352017645 22 57.0630098732821 2 4.06341627012807e-13 1.38156153184354e-10
19 103 Bmp4r Smad2 100 840.707556934809 22 45.5028049561182 2 1.31580524254105e-10 4.47373782463957e-08
20 87 Bmp4r Akt 0.99999986100714 840.881080149928 22 45.3292817409989 2 1.43506539984628e-10 4.87922235947735e-08

LA4:Mek->Raf

Model residual = 848

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 92 Bmp4r Fgfr 99.9999999998871 756.453012885639 23 91.0530470797144 2 0 0
2 402 Stat3 Akt 0.000876691542665974 761.643093740094 22 85.8629662252594 1 0 0
3 213 Jak Akt 0.000207877929489084 761.664819589532 22 85.8412403758214 1 0 0
4 414 Stat3 Pi3k 0.000662060815709944 763.651327388459 22 83.8547325768947 1 0 0
5 219 Jak Gsk3 0.000106137160274509 763.753513230211 22 83.7525467351428 1 0 0
6 408 Stat3 Gsk3 0.000188384138055831 763.793717539516 22 83.7123424258373 1 0 0
7 220 Jak Igfr 4.5094100900247e-05 763.823406873012 22 83.6826530923414 1 0 0
8 409 Stat3 Igfr 0.000298654168208828 763.961827327892 22 83.5442326374615 1 0 0
9 225 Jak Pi3k 0.000108900039270936 764.508275895523 22 82.9977840698309 1 0 0
10 415 Stat3 Raf -0.397915197814874 774.758983389517 22 72.7470765758368 1 0 0
11 412 Stat3 Mek -0.39791511745028 774.758983846823 22 72.7470761185308 1 0 0
12 416 Stat3 Ras -0.397915082545291 774.758984056642 22 72.7470759087117 1 0 0
13 227 Jak Ras -0.150413026212547 774.959016686801 22 72.5470432785526 1 0 0
14 226 Jak Raf -0.14984161917485 775.222156439718 22 72.2839035256358 1 0 0
15 223 Jak Mek -0.150301001709378 775.317600296257 22 72.188459669097 1 0 0
16 90 Bmp4r Erk 100.000000000402 785.08521508742 23 62.4208448779337 2 2.78665979180914e-14 9.44677669423298e-12
17 95 Bmp4r Jak 10.0001299400775 785.148219591524 23 62.3578403738298 2 2.87547763377916e-14 9.74786917851135e-12
18 96 Bmp4r Lifr 24.7014811331194 786.695326940284 23 60.8107330250697 2 6.23945339839338e-14 2.11517470205536e-11
19 103 Bmp4r Smad2 100 802.108709896285 23 45.3973500690688 2 1.38704492336217e-10 4.70208229019776e-08
20 97 Bmp4r Mek 99.9999999999469 802.209611798114 23 45.2964481672398 2 1.45881862145814e-10 4.94539512674309e-08

LA5:Jak->Gsk3

Model residual = 762

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 92 Bmp4r Fgfr 99.999999999999 681.029483559547 24 80.7186768658258 2 0 0
2 90 Bmp4r Erk 100.000000002215 698.975927953664 24 62.7722324717087 2 2.34257058195908e-14 7.91788856702169e-12
3 96 Bmp4r Lifr 20.1572550503172 708.879414934297 24 52.8687454910764 2 3.30901972489528e-12 1.1184486670146e-09
4 95 Bmp4r Jak 100.000000005454 708.985881831306 24 52.7622785940674 2 3.48987505560672e-12 1.17957776879507e-09
5 103 Bmp4r Smad2 100.000000000016 716.279768441786 24 45.4683919835873 2 1.33864141993456e-10 4.52460799937881e-08
6 100 Bmp4r Raf 99.9999999999111 716.848944902095 24 44.8992155232779 2 1.77934111889044e-10 6.01417298184969e-08
7 101 Bmp4r Ras 99.9999999999111 716.848944902095 24 44.8992155232779 2 1.77934111889044e-10 6.01417298184969e-08
8 97 Bmp4r Mek 99.9999999999111 716.848944903025 24 44.8992155223483 2 1.77934111889044e-10 6.01417298184969e-08
9 94 Bmp4r Igfr 100.000000047193 718.332054438826 24 43.4161059865468 2 3.73518771468184e-10 1.26249344756246e-07
10 87 Bmp4r Akt 0.09983217221069 718.338556530961 24 43.4096038944116 2 3.74735020791661e-10 1.26660437027581e-07
11 93 Bmp4r Gsk3 0.0999382044171066 718.342721356563 24 43.4054390688099 2 3.75516173711787e-10 1.26924466714584e-07
12 99 Bmp4r Pi3k 10.0000001026962 718.344750237288 24 43.4034101880849 2 3.75897313276141e-10 1.27053291887336e-07
13 208 Igfr Smad2 0.208058289157629 731.453411746761 23 30.2947486786123 1 3.71129329490572e-08 1.25441713367813e-05
14 187 Gsk3 Smad2 0.23636374954928 731.713440217495 23 30.0347202078779 1 4.24379312802259e-08 1.43440207727164e-05
15 313 Pi3k Smad2 0.291635842255944 731.735593106815 23 30.0125673185578 1 4.29255267997419e-08 1.45088280583128e-05
16 439 mTor Smad2 0.476359061820509 731.737253899431 23 30.0109065259417 1 4.29623070452578e-08 1.45212597812971e-05
17 61 Akt Smad2 0.110703876200108 731.755166772871 23 29.9929936525022 1 4.33610209960023e-08 1.46560250966488e-05
18 136 Fgf4 Igfr -0.000230030094384335 733.329954466968 23 28.4182059584047 1 9.77418065373215e-08 3.30367306096147e-05
19 141 Fgf4 Pi3k -6.94771512898917e-05 733.376118980697 23 28.3720414446757 1 1.0010056805676e-07 3.38339920031849e-05
20 129 Fgf4 Akt -0.000105606048312898 733.37962929227 23 28.3685311331027 1 1.00282242732064e-07 3.38953980434376e-05

LA6:Bmp4r->Fgf4

Model residual = 678

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 103 Bmp4r Smad2 1.0042272532134 636.33542723516 25 41.7743638116726 1 1.02437835991509e-10 3.45215507291385e-08
2 208 Igfr Smad2 0.249284149164735 644.510200809371 25 33.5995902374623 1 6.7706988904348e-09 2.28172552607653e-06
3 313 Pi3k Smad2 0.306164907558326 644.566687890486 25 33.5431031563468 1 6.97020896556211e-09 2.34896042139443e-06
4 187 Gsk3 Smad2 0.249806207463971 644.567930268484 25 33.541860778349 1 6.97466251420309e-09 2.35046126728644e-06
5 61 Akt Smad2 0.116406202163515 644.587455752443 25 33.5223352943897 1 7.045031447106e-09 2.37417559767472e-06
6 439 mTor Smad2 0.508103438434418 644.606227286278 25 33.5035637605554 1 7.11335346181841e-09 2.3972001166328e-06
7 338 Ras Actr 1 649.573170379612 25 28.5366206672211 1 9.19429569146146e-08 3.09847764802251e-05
8 149 Fgfr Actr 1 650.775568437361 25 27.3342226094724 1 1.71155250416888e-07 5.76793193904913e-05
9 250 Lifr Smad2 -0.231191116737432 654.476285711479 25 23.6335053353536 1 1.16540568284584e-06 0.000392741715119048
10 292 NoLif Smad2 -0.231090561903552 654.546306151978 25 23.5634848948549 1 1.20859425278841e-06 0.000407296263189694
11 418 Stat3 Smad2 0.153592104027131 655.110691367352 25 22.9990996794809 1 1.62077283738515e-06 0.000546200446198796
12 229 Jak Smad2 0.0200933153225715 655.491666537648 25 22.6181245091849 1 1.97611591612468e-06 0.000665951063734017
13 136 Fgf4 Igfr -0.00035295112549801 655.952924136683 25 22.1568669101503 1 2.51255654615257e-06 0.000846731556053416
14 264 Mek Lifr 1.66465270185779 656.000130722472 25 22.1096603243606 1 2.57510604795286e-06 0.000867810738160114
15 116 Erk Jak 0.379391979317811 656.021223883741 25 22.0885671630916 1 2.60355753312069e-06 0.000877398888661673
16 117 Erk Lifr 0.375244116388909 656.038688340346 25 22.0711027064867 1 2.62735296041594e-06 0.000885417947660172
17 135 Fgf4 Gsk3 -2.08252754578796e-05 656.335764496642 25 21.7740265501906 1 3.06724473619902e-06 0.00103366147609907
18 141 Fgf4 Pi3k -0.000121308673223279 656.563916875197 25 21.5458741716359 1 3.4546509503075e-06 0.00116421737025363
19 129 Fgf4 Akt -0.000318112962367812 656.630505604689 25 21.4792854421435 1 3.57671541484361e-06 0.0012053530948023
20 355 Ras Smad2 0.15111976561713 657.115485671446 25 20.9943053753871 1 4.60650537492668e-06 0.00155239231135029

LA7:Bmp4->Smad2

Model residual = 632

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 240 Lifr Gsk3 0.0143390210735803 608.76681530127 26 23.3350673035478 1 1.36095977620876e-06 0.000457282484806143
2 282 NoLif Gsk3 0.0140802719179266 608.767052400603 26 23.3348302042143 1 1.36112754733908e-06 0.000457338855905931
3 117 Erk Lifr 0.235333065436439 609.846777886993 26 22.2551047178251 1 2.38723290568732e-06 0.000802110256310939
4 116 Erk Jak 0.179360566858274 609.95569814019 26 22.1461844646282 1 2.5265761844917e-06 0.000848929597989211
5 264 Mek Lifr 0.734246984293458 609.959334424456 26 22.1425481803615 1 2.53136632533124e-06 0.000850539085311297
6 263 Mek Jak 0.593274881393048 609.96534675699 26 22.1365358478282 1 2.53930647076128e-06 0.00085320697417579
7 135 Fgf4 Gsk3 -2.80287166397671e-05 610.10622330949 26 21.9956592953274 1 2.73267788630793e-06 0.000918179769799464
8 141 Fgf4 Pi3k -8.23884179619931e-05 610.1476827275 26 21.9541998773176 1 2.79235155287161e-06 0.000938230121764861
9 293 NoLif Stat3 -0.632745208165191 612.344309787469 26 19.757572817349 1 8.79126644670603e-06 0.00295386552609323
10 251 Lifr Stat3 -0.63270717944737 612.344369282574 26 19.7575133222435 1 8.79154011779182e-06 0.00295395747957805
11 180 Gsk3 Lifr 0.867843142551938 612.628844233782 26 19.473038371036 1 1.02029724680097e-05 0.00342819874925126
12 53 Akt Jak 0.338443191181157 612.650128188719 26 19.4517544160983 1 1.0317302634788e-05 0.00346661368528877
13 179 Gsk3 Jak 0.706270694669131 612.67623863157 26 19.4256439732482 1 1.0459317639322e-05 0.00351433072681219
14 54 Akt Lifr 0.429718611485319 612.719356768399 26 19.3825258364188 1 1.06981478784629e-05 0.00359457768716353
15 200 Igfr Jak 1.0831051423795 613.780333597619 26 18.3215490071989 1 1.86584646959531e-05 0.00626924413784024
16 314 Pi3k Stat3 0.240200880301113 613.855318792569 26 18.2465638122486 1 1.94075742894206e-05 0.00652094496124532
17 62 Akt Stat3 0.0897158277781167 613.909534451161 26 18.1923481536563 1 1.99679475189063e-05 0.00670923036635252
18 188 Gsk3 Stat3 0.193318736418735 613.931722419491 26 18.1701601853269 1 2.02019438222401e-05 0.00678785312427267
19 440 mTor Stat3 0.386978549581844 613.935622383882 26 18.1662602209353 1 2.02433569462812e-05 0.00680176793395048
20 209 Igfr Stat3 0.228570594087011 614.400335021819 26 17.7015475829986 1 2.58416275378259e-05 0.0086827868527095

LA8:Gsk3->Lifr

Model residual = 613

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 404 Stat3 Bmp4r 0.989121487487614 589.221113168335 27 23.477590080666 1 1.26377276210565e-06 0.000423363875305393
2 129 Fgf4 Akt -5.79655757609428e-05 589.706320667404 27 22.9923825815974 1 1.62644575563142e-06 0.000544859328136526
3 141 Fgf4 Pi3k -8.24606437128686e-06 589.842008164571 27 22.8566950844297 1 1.74540282704694e-06 0.000584709947060725
4 136 Fgf4 Igfr -5.52936373962057e-05 589.862434635845 27 22.8362686131561 1 1.76405138752056e-06 0.000590957214819388
5 135 Fgf4 Gsk3 -2.49275193156912e-05 589.869865988431 27 22.8288372605706 1 1.77088538944048e-06 0.000593246605462561
6 250 Lifr Smad2 -0.210069735348591 590.002210840462 27 22.6964924085396 1 1.89713857801088e-06 0.000635541423633645
7 215 Jak Bmp4r 0.120785949035553 591.926400472532 27 20.7723027764692 1 5.17256538834499e-06 0.00173280940509557
8 240 Lifr Gsk3 0.000467030136082095 593.024135735067 27 19.6745675139338 1 9.18152287165963e-06 0.00307581016200598
9 251 Lifr Stat3 -0.602821731820639 593.274304858969 27 19.424398390032 1 1.04661412198004e-05 0.00350615730863313
10 234 Lifr Akt 0.00256829058134747 593.761950690896 27 18.936752558105 1 1.35124281616106e-05 0.00452666343413955
11 257 Mek Bmp4r 0.847167428869818 593.781604480977 27 18.9170987680246 1 1.36523509980391e-05 0.0045735375843431
12 246 Lifr Pi3k 0.0014329226801703 593.983953309066 27 18.7147499399347 1 1.51803687209462e-05 0.00508542352151698
13 241 Lifr Igfr 0.000312224089435361 594.080061154952 27 18.6186420940489 1 1.59651710182063e-05 0.00534833229109911
14 110 Erk Bmp4r 0.245999438964454 595.206705834924 27 17.4919974140774 1 2.8851957524112e-05 0.00966540577057752
15 418 Stat3 Smad2 0.135160968578516 595.836664898337 27 16.8620383506643 1 4.0197552229837e-05 0.0134661799969954
16 276 NoLif Akt 0.00099729091500089 596.196182228098 27 16.5025210209036 1 4.85854306955247e-05 0.0162761192830008
17 283 NoLif Igfr 0.000150217255013358 596.197146464117 27 16.501556784884 1 4.86101452280563e-05 0.0162843986513989
18 282 NoLif Gsk3 0.00037504000957938 596.199247867953 27 16.4994553810477 1 4.86640505452662e-05 0.0163024569326642
19 288 NoLif Pi3k 0.000140237702947237 596.202578696719 27 16.4961245522824 1 4.87496162971945e-05 0.0163311214595602
20 292 NoLif Smad2 -0.130419398730647 596.395619810129 27 16.3030834388721 1 5.39760499924657e-05 0.018081976747476

LA9:Jak->Bmp4

Model residual = 583

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 240 Lifr Gsk3 0.0114891463642068 559.526948317709 28 23.8854530671105 1 1.02241441168882e-06 0.000341486413504066
2 136 Fgf4 Igfr -0.000503037550874993 561.375736801401 28 22.0366645834184 1 2.67491636118944e-06 0.000893422064637273
3 234 Lifr Akt 0.00156698121367189 561.455440225706 28 21.9569611591132 1 2.78833683864388e-06 0.000931304504107056
4 141 Fgf4 Pi3k -7.0677192795186e-05 561.535531399745 28 21.8768699850746 1 2.90717039908017e-06 0.000970994913292777
5 129 Fgf4 Akt -0.000238059323482613 561.537476282811 28 21.8749251020085 1 2.91011841513367e-06 0.000971979550654646
6 135 Fgf4 Gsk3 -1.70288004584705e-05 561.551552536446 28 21.8608488483734 1 2.93154452868372e-06 0.000979135872580362
7 276 NoLif Akt 0.00350107720363554 561.668064423906 28 21.7443369609134 1 3.11508031924923e-06 0.00104043682662924
8 282 NoLif Gsk3 0.000654676464182579 561.862074679599 28 21.55032670522 1 3.44663966289627e-06 0.00115117764740735
9 288 NoLif Pi3k 0.000386483072890697 561.870668370546 28 21.5417330142728 1 3.46211875901226e-06 0.0011563476655101
10 246 Lifr Pi3k 0.000380277146911214 562.396419072152 28 21.0159823126673 1 4.55468047555474e-06 0.00152126327883528
11 241 Lifr Igfr 0.000337406796559118 562.668137322702 28 20.7442640621173 1 5.24885622821269e-06 0.00175311798022304
12 283 NoLif Igfr 0.000254654336528552 562.948556074729 28 20.4638453100901 1 6.07683624387345e-06 0.00202966330545373
13 189 Gsk3 mTor -41.382836597359 567.054178403313 28 16.3582229815058 1 5.24281932869908e-05 0.0175110165578549
14 262 Mek Igfr 0.000269872684451245 568.962445664801 28 14.4499557200179 1 0.000143933240347005 0.0480737022758997
15 267 Mek Pi3k 0.00020850486813912 569.063685473423 28 14.3487159113968 1 0.000151883248699192 0.0507290050655301
16 255 Mek Akt 0.000225008495847219 569.068548217125 28 14.3438531676942 1 0.000152276043511645 0.0508601985328894
17 260 Mek Fgfr 0.242854259531381 569.210583219689 28 14.2018181651301 1 0.000164211769053457 0.0548467308638546
18 324 Raf Gsk3 -0.000494423192421988 569.247964525497 28 14.1644368593224 1 0.000167506794934158 0.0559472695080088
19 318 Raf Akt -0.000776345820601977 569.262191629784 28 14.1502097550356 1 0.000168778286164462 0.0563719475789303
20 325 Raf Igfr -0.000529149826578222 569.262392658934 28 14.150008725885 1 0.000168796321823872 0.0563779714891732

LA10:Lifr->Gsk3

Model residual = 560

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 136 Fgf4 Igfr -0.0133454670728752 541.265608932434 29 18.259001352778 1 1.92812637936912e-05 0.00642066084329917
2 324 Raf Gsk3 -0.0247008725169053 541.319609708669 29 18.2050005765431 1 1.98357349417977e-05 0.00660529973561863
3 262 Mek Igfr 0.00599446593999118 541.416525597699 29 18.1080846875126 1 2.08713369717062e-05 0.00695015521157816
4 141 Fgf4 Pi3k -0.00815376560497824 541.423369753465 29 18.1012405317468 1 2.09464918951019e-05 0.00697518180106893
5 129 Fgf4 Akt -0.0181351148867678 541.501176788997 29 18.0234334962146 1 2.18202394788314e-05 0.00726613974645086
6 318 Raf Akt -0.0106487253424753 541.529540475377 29 17.9950698098344 1 2.21477834999595e-05 0.00737521190548651
7 330 Raf Pi3k 1 541.565846073237 29 17.9587642119748 1 2.2574259703867e-05 0.00751722848138771
8 267 Mek Pi3k 0.000266041920652527 541.603844910683 29 17.9207653745286 1 2.30294666665465e-05 0.00766881239995998
9 260 Mek Fgfr 0.299933930006755 541.606864796078 29 17.9177454891333 1 2.30660365618807e-05 0.00768099017510627
10 323 Raf Fgfr -0.951390831922905 541.609297078982 29 17.9153132062296 1 2.309553318669e-05 0.00769081255116777
11 255 Mek Akt 0.000650748621214826 541.6402443609 29 17.8843659243113 1 2.34741606310873e-05 0.00781689549015207
12 325 Raf Igfr -0.00166992058839143 541.655824083567 29 17.868786201645 1 2.36671261355514e-05 0.00788115300313862
13 261 Mek Gsk3 0.000123883858559426 541.725295543099 29 17.7993147421124 1 2.45471635291761e-05 0.00817420545521564
14 135 Fgf4 Gsk3 -0.000140538504213461 541.883902137858 29 17.6407081473535 1 2.66815617055993e-05 0.00888496004796457
15 257 Mek Bmp4r 5.79118062419735 542.846213728608 29 16.6783965566033 1 4.42824215746151e-05 0.0147460463843468
16 256 Mek Bmp4 1 542.892787230145 29 16.6318230550662 1 4.53831372757563e-05 0.0151125847128268
17 115 Erk Igfr 0.00165736427458077 543.338787224394 29 16.1858230608175 1 5.74222554801107e-05 0.0191216110748769
18 120 Erk Pi3k 0.000118282707856378 543.521737317127 29 16.0028729680848 1 6.324643449096e-05 0.0210610626854897
19 108 Erk Akt 0.000178915964434681 543.550949798081 29 15.9736604871305 1 6.42299341120367e-05 0.0213885680593082
20 114 Erk Gsk3 1.62722425691532e-05 543.613311857371 29 15.9112984278404 1 6.63812647423434e-05 0.0221049611592004

XO

Initial-Fit

Model residual = 1604

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 218 Jak Fgfr 31.1295786251237 1087.34331543124 17 516.380135495662 1 0 0
2 407 Stat3 Fgfr 56.8761121368597 1087.34331579986 17 516.38013512704 1 0 0
3 405 Stat3 Erk 0.814941998427444 1259.70107126248 17 344.022379664416 1 0 0
4 216 Jak Erk 0.694604520256767 1259.70107127177 17 344.022379655132 1 0 0
5 223 Jak Mek 0.153512506380784 1274.917666673 17 328.805784253903 1 0 0
6 226 Jak Raf 0.153512506380784 1274.917666673 17 328.805784253903 1 0 0
7 227 Jak Ras 0.153512506380784 1274.917666673 17 328.805784253903 1 0 0
8 412 Stat3 Mek 0.16923073826609 1274.91766667393 17 328.805784252966 1 0 0
9 415 Stat3 Raf 0.16923073826609 1274.91766667393 17 328.805784252966 1 0 0
10 416 Stat3 Ras 0.16923073826609 1274.91766667393 17 328.805784252966 1 0 0
11 281 NoLif Fgfr -26.1068432608996 1284.20827338603 17 319.515177540864 1 0 0
12 239 Lifr Fgfr -26.1068778185733 1284.20827338676 17 319.515177540144 1 0 0
13 279 NoLif Erk -1.09664018316424 1307.81404087304 17 295.909410053855 1 0 0
14 237 Lifr Erk -1.09664014791132 1307.8140408753 17 295.909410051596 1 0 0
15 286 NoLif Mek -0.239871680676967 1311.08678087291 17 292.636670053985 1 0 0
16 289 NoLif Raf -0.239871680676967 1311.08678087291 17 292.636670053985 1 0 0
17 290 NoLif Ras -0.239871680676967 1311.08678087291 17 292.636670053985 1 0 0
18 244 Lifr Mek -0.23987171324203 1311.08678087345 17 292.63667005345 1 0 0
19 247 Lifr Raf -0.23987171324203 1311.08678087345 17 292.63667005345 1 0 0
20 248 Lifr Ras -0.23987171324203 1311.08678087345 17 292.63667005345 1 0 0

LA1:Jak -> Fgfr

Model residual = 1064

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 118 Erk Mek -1.31339176786435 815.631614296276 18 247.924428705695 1 0 0
2 121 Erk Raf -1.31339176786435 815.631614296276 18 247.924428705695 1 0 0
3 122 Erk Ras -1.31339176786435 815.631614296276 18 247.924428705695 1 0 0
4 269 Mek Ras -5.83515826753276 815.631614445453 18 247.924428556518 1 0 0
5 268 Mek Raf -5.83502424986495 815.631614474367 18 247.924428527604 1 0 0
6 92 Bmp4r Fgfr 9.99999901889798 953.75111977238 19 109.804923229591 2 0 0
7 29 Actr Fgfr -0.107629858846352 960.885942451735 18 102.670100550236 1 0 0
8 386 Smad2 Fgfr -0.13808643958347 960.885942651532 18 102.670100350439 1 0 0
9 8 Activin Fgfr -0.107635962239693 960.885942683898 18 102.670100318073 1 0 0
10 97 Bmp4r Mek 0.999955073937196 962.159248396084 19 101.396794605887 2 0 0
11 100 Bmp4r Raf 0.999955073937196 962.159248396084 19 101.396794605887 2 0 0
12 101 Bmp4r Ras 0.999955073937196 962.159248396084 19 101.396794605887 2 0 0
13 179 Gsk3 Jak 0.109860902207229 962.880760270099 19 100.675282731872 2 0 0
14 180 Gsk3 Lifr 0.109860661919969 962.880760319587 19 100.675282682384 2 0 0
15 90 Bmp4r Erk 1.00653637430541 964.022332982434 19 99.5337100195376 2 0 0
16 6 Activin Erk -0.763290163155294 964.487925914488 18 99.0681170874832 1 0 0
17 27 Actr Erk -0.763290197639938 964.487925967266 18 99.0681170347048 1 0 0
18 384 Smad2 Erk -0.97912782463874 964.487926038699 18 99.0681169632721 1 0 0
19 391 Smad2 Mek -0.192631059168291 966.972716634667 18 96.5833263673039 1 0 0
20 394 Smad2 Raf -0.192631059168291 966.972716634667 18 96.5833263673039 1 0 0

LA2:Gsk3->Igfr

Model residual = 971

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 27 Actr Erk -0.727283543097939 872.469549801174 20 98.1627498106307 1 0 0
2 384 Smad2 Erk -1 872.724562869517 20 97.9077367422872 1 0 0
3 34 Actr Mek -0.151285797456677 875.395484707275 20 95.2368149045291 1 0 0
4 37 Actr Raf -0.151285797456677 875.395484707275 20 95.2368149045291 1 0 0
5 38 Actr Ras -0.151285797456677 875.395484707275 20 95.2368149045291 1 0 0
6 6 Activin Erk -1 876.192322542698 20 94.4399770691064 1 0 0
7 8 Activin Fgfr -0.109530713862061 877.034841976334 20 93.5974576354702 1 0 0
8 29 Actr Fgfr -0.10927737475233 877.039557710362 20 93.5927419014425 1 0 0
9 386 Smad2 Fgfr -0.100000056436587 880.796313125813 20 89.8359864859914 1 0 0
10 13 Activin Mek -0.1 885.337421121584 20 85.2948784902206 1 0 0
11 16 Activin Raf -0.1 885.337421121584 20 85.2948784902206 1 0 0
12 17 Activin Ras -0.1 885.337421121584 20 85.2948784902206 1 0 0
13 391 Smad2 Mek -0.1 894.489698566839 20 76.142601044965 1 0 0
14 394 Smad2 Raf -0.1 894.489698566839 20 76.142601044965 1 0 0
15 395 Smad2 Ras -0.1 894.489698566839 20 76.142601044965 1 0 0
16 260 Mek Fgfr -3.92518004852177 916.678502268416 20 53.9537973433884 1 2.05280237253191e-13 7.00005609033381e-11
17 113 Erk Fgfr -1.05151956744845 916.678504235341 20 53.9537953764636 1 2.05280237253191e-13 7.00005609033381e-11
18 409 Stat3 Igfr 0.000569673330190067 918.176414518159 20 52.4558850936455 1 4.3998138465895e-13 1.50033652168702e-10
19 32 Actr Jak -3.23493960849168 918.844000511234 20 51.7882991005704 1 6.18172180111287e-13 2.10796713417949e-10
20 11 Activin Jak -4.63137268134733 918.850333483499 20 51.7819661283057 1 6.20170581555612e-13 2.11478168310464e-10

LA3:Actr->Erk

Model residual = 872

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 268 Mek Raf -5.80340692432329 621.571326592804 21 250.774012313027 1 0 0
2 269 Mek Ras -5.94176876538838 621.617925550083 21 250.727413355747 1 0 0
3 118 Erk Mek -1.17821491553599 697.980244943352 21 174.365093962478 1 0 0
4 121 Erk Raf -1.17820871724599 697.980326416666 21 174.365012489165 1 0 0
5 122 Erk Ras -1.17820871724599 697.980326416666 21 174.365012489165 1 0 0
6 103 Bmp4r Smad2 10.0000005096801 796.15674199636 22 76.1885969094701 2 0 0
7 408 Stat3 Gsk3 0.118633710937965 816.354794412507 21 55.990544493323 1 7.28306304154103e-14 2.47624143412395e-11
8 219 Jak Gsk3 0.0988937639129446 816.354795064877 21 55.9905438409537 1 7.28306304154103e-14 2.47624143412395e-11
9 260 Mek Fgfr -3.53128900418508 816.518082598318 21 55.8272563075129 1 7.91589016557737e-14 2.69140265629631e-11
10 225 Jak Pi3k 0.00841361750060281 819.117407749582 21 53.2279311562482 1 2.96984659087229e-13 1.00974784089658e-10
11 220 Jak Igfr 0.00108015166043726 819.11769605947 21 53.2276428463607 1 2.97095681389692e-13 1.01012531672495e-10
12 414 Stat3 Pi3k 0.0132678791617126 819.124183213332 21 53.2211556924989 1 2.97983859809392e-13 1.01314512335193e-10
13 409 Stat3 Igfr 0.00205091522329278 819.126203233392 21 53.2191356724386 1 2.9831692671678e-13 1.01427755083705e-10
14 402 Stat3 Akt 0.000326549398621431 819.135505431363 21 53.2098334744672 1 2.99760216648792e-13 1.01918473660589e-10
15 213 Jak Akt 0.000139289032578143 819.136679190375 21 53.2086597154552 1 2.99982261253717e-13 1.01993968826264e-10
16 92 Bmp4r Fgfr 99.9999999999633 819.919256308247 22 52.4260825975837 2 4.12880840627849e-12 1.40379485813469e-09
17 416 Stat3 Ras -0.929015757404131 820.231193079124 21 52.1141458267064 1 5.23692200715686e-13 1.78055348243333e-10
18 226 Jak Raf -0.770240229659703 820.232598646607 21 52.1127402592235 1 5.24025267623074e-13 1.78168590991845e-10
19 412 Stat3 Mek -0.927587717145173 820.232782580777 21 52.1125563250531 1 5.24136289925536e-13 1.78206338574682e-10
20 227 Jak Ras -0.765032034178087 820.238248770425 21 52.1070901354051 1 5.25579579857549e-13 1.78697057151567e-10

LA4:Mek->Raf

Model residual = 622

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 103 Bmp4r Smad2 9.99999999837333 543.943194665216 23 77.6184579517288 2 0 0
2 219 Jak Gsk3 0.102202070590831 559.055830180669 22 62.5058224362759 1 2.66453525910038e-15 9.03277452835029e-13
3 408 Stat3 Gsk3 0.11896875623134 559.055830181284 22 62.5058224356602 1 2.66453525910038e-15 9.03277452835029e-13
4 220 Jak Igfr 0.000925261769832483 561.915250210237 22 59.6464024067076 1 1.13242748511766e-14 3.83892917454887e-12
5 414 Stat3 Pi3k 0.0102824036965262 561.918478963089 22 59.6431736538558 1 1.13242748511766e-14 3.83892917454887e-12
6 225 Jak Pi3k 0.00380468975561332 561.923168190086 22 59.6384844268587 1 1.14352971536391e-14 3.87656573508366e-12
7 402 Stat3 Akt 0.000183979611725293 561.925610102184 22 59.6360425147606 1 1.14352971536391e-14 3.87656573508366e-12
8 409 Stat3 Igfr 0.000686188976651362 561.930307671478 22 59.6313449454669 1 1.14352971536391e-14 3.87656573508366e-12
9 213 Jak Akt 0.000481629955883261 561.947020983964 22 59.6146316329805 1 1.15463194561016e-14 3.91420229561844e-12
10 412 Stat3 Mek -5.42574424914135 563.539523719549 22 58.022128897396 1 2.58681964737661e-14 8.76931860460671e-12
11 416 Stat3 Ras -5.27892674345496 563.706580677934 22 57.8550719390104 1 2.8199664825479e-14 9.55968637583738e-12
12 227 Jak Ras -4.41467488394102 563.763873033911 22 57.7977795830335 1 2.90878432451791e-14 9.86077886011572e-12
13 415 Stat3 Raf -5.18510183568 563.847122225534 22 57.7145303914109 1 3.03090885722668e-14 1.02747810259984e-11
14 223 Jak Mek -4.18913164829838 564.142064620446 22 57.4195879964988 1 3.51940698806175e-14 1.19307896895293e-11
15 226 Jak Raf -4.11883932261725 564.281653652771 22 57.2799989641737 1 3.77475828372553e-14 1.27964305818295e-11
16 92 Bmp4r Fgfr 9.99999999996672 564.667754286874 23 56.8938983300709 2 4.422018307082e-13 1.4990642061008e-10
17 100 Bmp4r Raf 10.0000000003232 569.112417084538 23 52.449235532407 2 4.08129086082454e-12 1.38355760181952e-09
18 101 Bmp4r Ras 10.0000000003232 569.112417084538 23 52.449235532407 2 4.08129086082454e-12 1.38355760181952e-09
19 97 Bmp4r Mek 10.0000000003232 569.112417087143 23 52.4492355298013 2 4.08129086082454e-12 1.38355760181952e-09
20 90 Bmp4r Erk 100 575.218164296974 23 46.3434883199707 2 8.64249782850379e-11 2.92980676386278e-08

LA5:Jak ->Gsk3

Model residual = 559

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 103 Bmp4r Smad2 10.0000028575307 477.713115752296 24 81.3427113077995 2 0 0
2 92 Bmp4r Fgfr 1.00056335622367 497.907615561665 24 61.1482114984304 2 5.27355936696949e-14 1.78246306603569e-11
3 97 Bmp4r Mek 0.997629454524129 500.331227637781 24 58.7245994223152 2 1.77080572427712e-13 5.98532334805666e-11
4 100 Bmp4r Raf 0.997629456543337 500.331227637871 24 58.7245994222246 2 1.77080572427712e-13 5.98532334805666e-11
5 101 Bmp4r Ras 0.997629456543337 500.331227637871 24 58.7245994222246 2 1.77080572427712e-13 5.98532334805666e-11
6 90 Bmp4r Erk 0.100423099077646 506.745499965664 24 52.3103270944316 2 4.37483382853543e-12 1.47869383404498e-09
7 237 Lifr Erk -0.822270522715082 517.01272195258 23 42.0431051075159 1 8.92834695065403e-11 3.01778126932106e-08
8 279 NoLif Erk -0.822270348744228 517.012721956798 23 42.0431051032974 1 8.92834695065403e-11 3.01778126932106e-08
9 96 Bmp4r Lifr 12.5474080562728 517.488872513285 24 41.5669545468112 2 9.41565381218368e-10 3.18249098851808e-07
10 95 Bmp4r Jak 1.01147394374831 517.488872562818 24 41.5669544972777 2 9.4156549224067e-10 3.18249136377346e-07
11 208 Igfr Smad2 0.187832193919486 524.010078615426 23 35.0457484446697 1 3.22049364953614e-09 1.08852685354322e-06
12 187 Gsk3 Smad2 0.186824426627274 524.280575809466 23 34.7752512506295 1 3.70047770203996e-09 1.25076146328951e-06
13 179 Gsk3 Jak 0.206210904964207 524.610301320383 23 34.4455257397126 1 4.38349290199369e-09 1.48162060087387e-06
14 180 Gsk3 Lifr 0.206201216611251 524.610301593093 23 34.4455254670024 1 4.3834934571052e-09 1.48162078850156e-06
15 188 Gsk3 Stat3 0.162578270369673 525.409116844457 23 33.6467102156384 1 6.60865517865261e-09 2.23372545038458e-06
16 439 mTor Smad2 0.384465354023658 525.93134008061 23 33.1244869794858 1 8.6443198155095e-09 2.92178009764221e-06
17 61 Akt Smad2 0.469967996091489 525.931340181637 23 33.1244868784585 1 8.64432025959871e-09 2.92178024774436e-06
18 313 Pi3k Smad2 0.0118701032847729 525.931340667699 23 33.1244863923968 1 8.64432248004476e-09 2.92178099825513e-06
19 418 Stat3 Smad2 0.15873962230718 526.235440601276 23 32.8203864588203 1 1.010792138878e-08 3.41647742940764e-06
20 229 Jak Smad2 0.142611672046156 526.235440620826 23 32.8203864392699 1 1.010792138878e-08 3.41647742940764e-06

LA6:Bmp4r->Fgfr

Model residual = 498

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 103 Bmp4r Smad2 3.55760900440195 416.56490425142 25 81.3427112265715 1 0 0
2 376 Smad1 Smad2 1 416.564904266311 25 81.3427112116806 1 0 0
3 86 Bmp4r Actr 1 418.66560709066 25 79.2420083873311 1 0 0
4 355 Ras Smad2 0.891548497978237 442.452509126299 25 55.4551063516919 1 9.5590202420226e-14 3.22138982156162e-11
5 166 Fgfr Smad2 0.89154916112959 442.452509274865 25 55.4551062031262 1 9.5590202420226e-14 3.22138982156162e-11
6 338 Ras Actr 1 442.523477371784 25 55.384138106207 1 9.91429160990265e-14 3.34111627253719e-11
7 149 Fgfr Actr 1 442.523477401559 25 55.3841380764324 1 9.91429160990265e-14 3.34111627253719e-11
8 107 Erk Actr 1 448.148378048923 25 49.7592374290678 1 1.73816516735315e-12 5.85761661398012e-10
9 124 Erk Smad2 0.123813580482007 448.148378050148 25 49.7592374278436 1 1.73816516735315e-12 5.85761661398012e-10
10 254 Mek Actr 1 448.148378135284 25 49.7592373427073 1 1.73816516735315e-12 5.85761661398012e-10
11 271 Mek Smad2 0.52849191438364 448.148378199061 25 49.7592372789301 1 1.73816516735315e-12 5.85761661398012e-10
12 208 Igfr Smad2 0.2046110173044 459.661831486638 25 38.2457839913535 1 6.2371685594087e-10 2.10192580452073e-07
13 187 Gsk3 Smad2 0.197944870904941 459.76223058369 25 38.1453848943012 1 6.56648735386511e-10 2.21290623825254e-07
14 61 Akt Smad2 0.501902047143557 460.982410477652 25 36.9252050003387 1 1.22748811115514e-09 4.13663493459282e-07
15 439 mTor Smad2 0.41055229726301 460.982410517205 25 36.9252049607862 1 1.22748811115514e-09 4.13663493459282e-07
16 313 Pi3k Smad2 0.0158669599140266 460.982410931451 25 36.9252045465403 1 1.22748833319974e-09 4.13663568288312e-07
17 180 Gsk3 Lifr 0.199732647674023 462.377582759657 25 35.5300327183345 1 2.51148313257232e-09 8.46369815676872e-07
18 179 Gsk3 Jak 0.199732102751562 462.377583070696 25 35.530032407295 1 2.51148357666153e-09 8.46369965334936e-07
19 237 Lifr Erk -0.764966358870349 463.036477423487 25 34.8711380545043 1 3.52264228897781e-09 1.18713045138552e-06
20 279 NoLif Erk -0.764965860588336 463.036477468898 25 34.8711380090929 1 3.52264240000011e-09 1.18713048880004e-06

LA7:Bmp4r->Smad2

Model residual = 417

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 179 Gsk3 Jak 0.199732765202077 381.03487161926 26 35.5300325504302 1 2.51148335461693e-09 8.43858407151289e-07
2 180 Gsk3 Lifr 0.199732867287141 381.034871788498 26 35.5300323811923 1 2.51148357666153e-09 8.43858481758274e-07
3 237 Lifr Erk -0.764965034366116 381.693766150894 26 34.8711380187967 1 3.52264240000011e-09 1.18360784640004e-06
4 279 NoLif Erk -0.764963421407936 381.693766167712 26 34.8711380019784 1 3.52264240000011e-09 1.18360784640004e-06
5 188 Gsk3 Stat3 0.161244470769444 382.79288139763 26 33.77202277206 1 6.19635942555874e-09 2.08197676698774e-06
6 201 Igfr Lifr 0.319995585724839 384.887884096662 26 31.6770200730288 1 1.82063796261289e-08 6.11734355437931e-06
7 200 Igfr Jak 0.319978108996516 384.88788421069 26 31.6770199590001 1 1.82063806253296e-08 6.11734389011075e-06
8 209 Igfr Stat3 0.230922270318018 388.046855489264 26 28.5180486804268 1 9.28291075119603e-08 3.11905801240187e-05
9 234 Lifr Akt 0.0462486835882535 389.947901693182 26 26.617002476508 1 2.48051196805044e-07 8.33452021264948e-05
10 276 NoLif Akt 0.0462490541301101 389.947901695643 26 26.6170024740474 1 2.48051197027088e-07 8.33452022011016e-05
11 241 Lifr Igfr 0.135730277444265 390.500983864222 26 26.0639203054685 1 3.30298833839393e-07 0.000110980408170036
12 283 NoLif Igfr 0.135713941481618 390.500983880051 26 26.0639202896396 1 3.30298836503928e-07 0.00011098040906532
13 246 Lifr Pi3k 1.54343726136456 390.596032053466 26 25.9688721162242 1 3.46966925413028e-07 0.000116580886938777
14 288 NoLif Pi3k 1.54343770696581 390.596032055373 26 25.9688721143174 1 3.46966925857117e-07 0.000116580887087991
15 282 NoLif Gsk3 0.122743900310306 390.752274218429 26 25.8126299512616 1 3.76218570297127e-07 0.000126409439619835
16 240 Lifr Gsk3 0.122742824007583 390.75227422112 26 25.8126299485701 1 3.76218570741216e-07 0.000126409439769049
17 54 Akt Lifr 0.554104230049228 392.653984070323 26 23.9109200993672 1 1.00897798327448e-06 0.000339016602380225
18 432 mTor Lifr 0.455535701154435 392.653984103547 26 23.910920066143 1 1.00897800059396e-06 0.000339016608199571
19 53 Akt Jak 0.55411025192976 392.653984269377 26 23.9109199003137 1 1.00897808752443e-06 0.000339016637408208
20 305 Pi3k Jak 0.0172865546228637 392.653984271849 26 23.910919897841 1 1.00897808885669e-06 0.000339016637855848

LA8:Gsk3->Lifr

Model residual = 381

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 279 NoLif Erk -0.764393641405135 346.640267272023 27 34.3946039717749 1 4.4996907311301e-09 1.50739639492858e-06
2 237 Lifr Erk -0.671915131243528 350.59628231404 27 30.4385889297583 1 3.4460443609774e-08 1.15442486092743e-05
3 403 Stat3 Bmp4 1 358.136223408382 27 22.8986478354155 1 1.70771942820114e-06 0.000572086008447382
4 404 Stat3 Bmp4r 5.16694532035676 358.13622342884 27 22.8986478149576 1 1.70771944629777e-06 0.000572086014509753
5 214 Jak Bmp4 1 358.136224971872 27 22.8986462719258 1 1.70772081720116e-06 0.000572086473762389
6 215 Jak Bmp4r 4.64938470945433 358.136225015044 27 22.8986462287534 1 1.70772085561488e-06 0.000572086486630985
7 282 NoLif Gsk3 0.318436289159327 359.190278164771 27 21.8445930790269 1 2.95648519665903e-06 0.000990422540880775
8 240 Lifr Gsk3 0.311248088346778 359.857519906772 27 21.1773513370257 1 4.18683105241069e-06 0.00140258840255758
9 290 NoLif Ras -1.00307161679687 360.854474073578 27 20.18039717022 1 7.04714154042829e-06 0.00236079241604348
10 286 NoLif Mek -1.00307388673015 360.854474079895 27 20.1803971639024 1 7.04714156363195e-06 0.0023607924238167
11 289 NoLif Raf -1.00307385371388 360.854474106585 27 20.1803971372126 1 7.04714166199771e-06 0.00236079245676923
12 234 Lifr Akt 0.0861744520773406 361.386146996292 27 19.6487242475058 1 9.30654265229869e-06 0.00311769178852006
13 276 NoLif Akt 0.0852495776128229 361.48224878615 27 19.5526224576483 1 9.78663001738322e-06 0.00327852105582338
14 418 Stat3 Smad2 0.123489181061212 361.498002703746 27 19.5368685400515 1 9.86766962174368e-06 0.00330566932328413
15 229 Jak Smad2 0.111176938966702 361.498002901528 27 19.5368683422702 1 9.86767064337091e-06 0.00330566966552926
16 405 Stat3 Erk 0.579528852131833 362.225890860039 27 18.8089803837588 1 1.44485208138923e-05 0.00484025447265392
17 216 Jak Erk 0.422591090041009 362.225890863 27 18.8089803807983 1 1.44485208363188e-05 0.0048402544801668
18 246 Lifr Pi3k 2.68468123206151 363.111707894694 27 17.9231633491037 1 2.30004694207198e-05 0.00770515725594113
19 288 NoLif Pi3k 19.0568961103352 363.111708544283 27 17.9231626995153 1 2.30004772707737e-05 0.00770515988570919
20 283 NoLif Igfr 0.264980298493324 363.164476191355 27 17.8703950524431 1 2.36471258477922e-05 0.00792178715901039

LA9:Jak->Bmp4r

Model residual = 358

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 279 NoLif Erk -0.769638285591323 322.674101698163 28 35.4621215369229 1 2.60058941048413e-09 8.68596863101699e-07
2 237 Lifr Erk -0.67618579083019 326.718024875319 28 31.4181983597674 1 2.08021984082762e-08 6.94793426836425e-06
3 282 NoLif Gsk3 0.313266646312437 336.487646298766 28 21.6485769363194 1 3.27452855275467e-06 0.00109369253662006
4 289 NoLif Raf -1.02517373826448 336.797778611651 28 21.3384446234345 1 3.84933968367029e-06 0.00128567945434588
5 286 NoLif Mek -1.02517394244013 336.79777861864 28 21.3384446164462 1 3.8493396976591e-06 0.00128567945901814
6 290 NoLif Ras -1.02517997083255 336.797779352587 28 21.3384438824985 1 3.84934117136915e-06 0.0012856799512373
7 240 Lifr Gsk3 0.306396102353566 337.150079546007 28 20.9861436890789 1 4.62617121088638e-06 0.00154514118443605
8 234 Lifr Akt 0.085820689251494 338.62289141259 28 19.5133318224958 1 9.99000173407261e-06 0.00333666057918025
9 276 NoLif Akt 0.084893980757223 338.721129015554 28 19.4150942195316 1 1.05172531232878e-05 0.00351276254317813
10 405 Stat3 Erk 0.579962297809042 339.315099455794 28 18.8211237792921 1 1.4356822449324e-05 0.00479517869807422
11 216 Jak Erk 0.444479524515352 339.315099573867 28 18.8211236612191 1 1.43568233380575e-05 0.0047951789949112
12 281 NoLif Fgfr -0.108383484219763 340.35436192307 28 17.7818613120164 1 2.47733778766523e-05 0.00827430821080187
13 246 Lifr Pi3k 23.2030125082974 340.365789763288 28 17.7704334717984 1 2.49226280025772e-05 0.00832415775286078
14 288 NoLif Pi3k 19.0182480124703 340.365789840598 28 17.7704333944877 1 2.49226290153226e-05 0.00832415809111775
15 283 NoLif Igfr 0.263028737857811 340.433553236296 28 17.7026699987904 1 2.58263839479911e-05 0.00862601223862903
16 241 Lifr Igfr 0.263035652900652 340.433554821261 28 17.7026684138252 1 2.58264054671109e-05 0.00862601942601504
17 136 Fgf4 Igfr -0.330801963069541 341.321935492972 28 16.8142877421137 1 4.1221770744948e-05 0.0137680714288126
18 141 Fgf4 Pi3k -20.808366348189 341.382338630865 28 16.7538846042204 1 4.2555050730031e-05 0.0142133869438304
19 248 Lifr Ras -0.855984413753137 342.75537862185 28 15.3808446132356 1 8.7874612522576e-05 0.0293501205825404
20 244 Lifr Mek -0.855977114510201 342.75537882371 28 15.3808444113757 1 8.78746219103999e-05 0.0293501237180736

LA10:Lifr->Gsk3

Model residual = 337

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 279 NoLif Erk -0.750107662459603 305.145157578298 29 32.0049217109288 1 1.53782467871011e-08 5.12095618010467e-06
2 237 Lifr Erk -0.710878870095384 308.100362579255 29 29.0497167099725 1 7.05444163084934e-08 2.34912906307283e-05
3 216 Jak Erk 0.648996943299005 318.468331829937 29 18.6817474592897 1 1.54453947721622e-05 0.00514331645913001
4 405 Stat3 Erk 0.563776705884382 318.468332131869 29 18.6817471573583 1 1.54453972178725e-05 0.00514331727355154
5 281 NoLif Fgfr -0.106154268904962 319.089496992204 29 18.0605822970235 1 2.1398594252986e-05 0.00712573188624434
6 290 NoLif Ras -0.976634438478416 319.154377438167 29 17.9957018510606 1 2.21404311442353e-05 0.00737276357103036
7 286 NoLif Mek -0.97664618670698 319.154377500559 29 17.9957017886678 1 2.2140431869877e-05 0.00737276381266904
8 289 NoLif Raf -0.97664450331774 319.154377711864 29 17.9957015773637 1 2.21404343274667e-05 0.00737276463104641
9 136 Fgf4 Igfr -0.258919130634636 323.058387920278 29 14.0916913689487 1 0.000174111179582659 0.0579790228010255
10 141 Fgf4 Pi3k -4.64938848212688 323.166921742145 29 13.9831575470826 1 0.000184455575801823 0.0614237067420071
11 247 Lifr Raf -0.884873837288881 323.928308429415 29 13.221770859812 1 0.000276716049664505 0.0921464445382802
12 248 Lifr Ras -0.88487265763921 323.92830843157 29 13.2217708576568 1 0.000276716049982695 0.0921464446442374
13 244 Lifr Mek -0.884880637090151 323.92830848693 29 13.2217708022974 1 0.000276716058155824 0.0921464473658894
14 135 Fgf4 Gsk3 -0.141553149825423 323.98117630589 29 13.1689029833371 1 0.000284633319800331 0.0947828954935102
15 239 Lifr Fgfr -0.102266153684203 324.101991649728 29 13.0480876394996 1 0.000303594239811522 0.101096881857237
16 129 Fgf4 Akt -0.0574139184341608 325.327875053988 29 11.8222042352394 1 0.000585285303497107 0.194900006064537
17 137 Fgf4 Jak -0.0940410228474239 325.795687867084 29 11.354391422143 1 0.000752697815567638 0.250648372584023
18 275 NoLif Actr 1 325.908349382738 29 11.2417299064888 1 0.000799785782001461 0.266328665406487
19 233 Lifr Actr 1 326.092378645092 29 11.0577006441351 1 0.000883196052319013 0.294104285422231
20 305 Pi3k Jak -0.0216203288565324 326.1172869811 29 11.0327923081269 1 0.000895142139000438 0.298082332287146

Summary

Links Added and Residuals

Model_iteration Links res_p_05_XX res_p_05_XO
1 Init Init Network 2056.3 1603.72
2 1 Jak->Fgfr 1515 1063.56
3 2 Gsk3->Igfr 971.06 970.63
4 3 Actr->Erk 886.21 872.35
5 4 Mek->Raf 847.51 621.56
6 5 Jak->Gsk3 761.75 559.06
7 6 Bmp4r->Fgfr 678.11 497.91
8 7 Bmp4r->Smad2 632.1 416.56
9 8 Gsk3->Lifr 612.7 381.03
10 9 Jak->Bmp4r 583.41 358.14
11 10 Lifr->Gsk3 559.52 337.15